Head coach Jim Harbaugh played a big part in quarterback Alex Smith and the rest of the 49ers’ breakthrough season in his first year. To view more photos visit www.StuJosseyPhotography.com.

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SANTA CLARA — Jim Harbaugh arrived as the new coach of the 49ers a year ago challenged with turning around San Francisco’s once-proud franchise in the midst of a lockout and minus the usual offseason preparation time with his players.

He did it, and then some. And he did it his own blue-collar, rah-rah way.

Even Harbaugh acknowledged Monday it was no easy accomplishment. A day after his team lost the NFC championship game 20-17 in overtime to the New York Giants to miss a chance at the Super Bowl, Harbaugh regrouped and told his team how proud he is of this special season.

“Who’s got it better than us? No-body!” became a mantra for the NFC West champions (14-4), who ended an eight-year stretch without a playoff berth or winning record and then became a surprise participant in the NFC title game after beating Drew Brees and the Saints in the divisional round.

“I’ve said so often how proud I was of this team. I thought they played their hearts out. I thought we were a well-coached team. Be very proud of our guys. They stand toe-to-toe and fight every time they go out onto the field. It didn’t have the ending that we wanted. The football gods had a different ending in mind for this ball game.”

Harbaugh took a double hit after big brother, John, and the Baltimore Ravens lost Sunday’s first game to New England. No “Superbaugh” this year.

“That was another painful thing,” Harbaugh said.

As he looks back, Harbaugh can point to all the progress made with a roster featuring only a handful of new faces from the group that went 6-10 last season and saw coach Mike Singletary fired with one week left.

Harbaugh, the 15-year NFL quarterback, left Stanford for a chance to prove he could coach at the highest level. He made it clear he didn’t care to make friends along the way, aside from in his own building.

After a win at previously unbeaten Detroit on Oct. 16, Harbaugh made headlines for his second-long handshake and backslap with Jim Schwartz that infuriated the Lions coach. Harbaugh’s response in the aftermath when asked about reaching out to Schwartz: “Apologies seem like excuses.”

And Harbaugh offered no excuses Monday after his Niners missed many opportunities to win. Kyle Williams lost his second fumble in overtime, setting up Lawrence Tynes’ winning field goal.

“It’s tough,” said running back Frank Gore, who became the franchise rushing leader last month. “It’s over. We’ve got to move on. I know we’ve got a great group of guys in here, guys who work hard, a coaching staff that works hard. We’ll get back.”

San Francisco fell short 30 years after the Niners’ two-decade run began under the late Bill Walsh with the first of five Super Bowl championships. Harbaugh used some of the same methods as the Hall of Fame coach and his unique version of Walsh’s West Coast offense.

“The main symmetry between the teams is sort of coincidental but not really — getting the coach from Stanford that we did back in ‘79 and the Niners did here this year has made just a huge difference in the culture and the winning attitude and the approach of this football team,” former 49ers offensive lineman Randy Cross said .

“I guess it’s simplistic to credit just one person — because it’s never just one person. They were really looking for the individual who was going to kind of take that place by the scruff of the neck and drag it into this decade and form it in sort of his vision. They thought various people along the way were that guy but they found it in Jim.”

San Francisco’s defense ranked No. 1 against the run and allowed only three touchdowns rushing and all in the final two games — and the Niners had 38 takeaways to only 10 turnovers for a plus-28 turnover differential. That matched the second-best mark in NFL history since 1941.

“We let an opportunity get away from us, one of those chances that don’t come around often,” All-Pro linebacker Patrick Willis said. “It hadn’t been around here for a while and we let it slip away from us. Only time will heal that. ... I don’t believe in moral victories. There’s a lot we can look back on and be thankful about, considering where we have been in the past; there’s a lot of positives we can build on.”

The 49ers plan to bring back quarterback Alex Smith, the 2005 No. 1 overall draft pick who orchestrated five comeback wins during the regular season — four of those on the road — and another in a thrilling 36-32 victory against the Saints. Smith threw just five interceptions and thrived under Harbaugh.

Neither Harbaugh nor Smith offered any kind of timeline for when something might get done in regards to a new contract, though Smith will be rewarded with a raise and multiyear deal. He made $4.9 million in base salary this season plus earned a $1 million bonus for reaching the playoffs.

Both sides are committed to getting something done — in time, after everybody decompresses a bit.

“Not in a crazy rush at this point. Take our time a little bit. I think I have until March 13, that’s when the contract is up,” Smith said. “I love it here. I love what’s going on, I love this team the coaching staff, I love everything about it. No question I want to stay.”

General manager Trent Baalke also faces key decisions with free agents such as cornerback Carlos Rogers, wideout and return man Ted Ginn Jr., linebacker Ahmad Brooks and safety Dashon Goldson. The team has expressed a commitment to re-signing injured wide receiver Joshua Morgan, who was lost for the season in early October to a broken right leg that required surgery.

“My preference is to be back,” said Rogers, who had six interceptions in the regular season.